Welcome in the PCTG R Markdown template. This document describes how the template looks like, building an interactive Manhattan plot.
Let’s load a GWAS summary statistic stored in the qqman library. This library is:
It’s often handy to keep a trace of the raw data somewhere in your document. The DT library allows to build interactive tables that you can search, filter, highlight and more.
Using HTML outputs you can embed some interactive graphics. For example, the plotly library can transform any of your ggplot2 graphic in an interactive chart:
# Make the plot
p <- ggplot(don, aes(x=BPcum, y=-log10(P), text=text)) +
# Show all points
geom_point( aes(color=as.factor(CHR)), alpha=0.8, size=1.3) +
scale_color_manual(values = rep(c("grey", "#69b3a2"), 22 )) +
# custom X axis:
scale_x_continuous( label = axisdf$CHR, breaks= axisdf$center ) +
scale_y_continuous(expand = c(0, 0) ) + # remove space between plot area and x axis
# Add highlighted points
geom_point(data=subset(don, is_highlight=="yes"), color="orange", size=2) +
# Custom the theme:
theme_bw() +
theme(
legend.position="none",
panel.border = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank()
) +
ylim(0, 10)
ggplotly(p, tooltip="text")A work by Yan Holtz